PathCase Desktop Client

The PathCase Desktop Client (rich desktop client) is a desktop application for browsing and interacting with the PathCase database, and includes a richer set of tools as compared to the PathCase Web Client. However, (a) the Desktop Client needs to be downloaded and installed at the user desktop, and (b) its use requires the installations at the desktop client machine (i) Microsoft .Net framework 1.1 (see below for download instructions), (ii) Microsoft Data Access Components (MDAC) Version 2.6 or higher (see below for download instructions), and (iii) a commercial graphics library, and the accompanying licence from Tom Sawyer Software (please visit the Tom Sawyer Software website and inquire directly for a licence).

The latest version of PathCase Desktop Client (Version 2.0) was released in July, 2004. Since then, the desktop client has not been revised, and our developments have (and will continue to be) concentrated on the web client.

Components

• Metabolic Pathway Browser: A tree viewer to browse metabolic pathways at pathway, process, and molecular entity levels
• Signaling Pathway Browser: A tree viewer to browse signaling pathways at pathway, signaling step, and molecular entity levels
• Pathway Viewer: A graphical tool to view and edit pathway graphs and genes
• Pathway Explorer: A tree-structured query interface
• Pathway Editor: A plug-in tool to create and update pathways
• Pathway Web Services: An XML web service to query the pathway database
• J-Viewer: A Java version of the graphical tool to view pathway graphs

User Manuals

• "Pathways Database System Release 2.0 - Overview", Report, Computational Genomics Center, EECS and Genetics Departments, CWRU, July, 2004
• "Pathway Viewer Tool -- Release #2", User Manual, Computational Genomics Center, EECS and Genetics Departments, CWRU, July 2004
• "Pathway Explorer -- Release #2", User Manual, Computational Genomics Center, EECS and Genetics Departments, CWRU, July 2004
• "Pathway Editor Tool -- Release #2", User Manual, Computational Genomics Center, EECS and Genetics Departments, CWRU, July 2004
• "Pathway Querying Services -- Release #2", User Manual, Computational Genomics Center, EECS and Genetics Departments, CWRU, July 2004
• " J-Pathways Viewer", User Manual, Computational Genomics Center, EECS and Genetics Departments, CWRU, Dec. 2003

Download and Installation

• What’s new for release 2.0?

The use of this component requires a Tom Sawyer licence. Please contact http://www.tomsawyer.com directly for a licence. To revise the steps of the desktop client installation, please contact us (pathway \at\ eecs \dot\ case \dot\ edu).

J-Pathway Viewer, released in July, 2003 (J-Viewer installation guide)

System requirements

1. Operating system: Windows 2000 or Windows XP
2. Processor: Intel Pentium III 600MHz and above RAM: 256M and above
3. Network connection: 56k and above

Software requirements

1. Microsoft .NET framework 1.1.

   .NET framework redistributable 1.1 can be downloaded from here (23.1M bytes). If you run windows update regularly, you most likely have .Net framework 1.1 installed. You can check it by clicking: Control panel->Add/remove software.

2. Microsoft Data Access Components (MDAC) Version 2.6 or higher.

   This software can be downloaded from here (5.13M bytes). If you have a full version of .NET installed or if you have a SQL 2000 installed, you can skip this step.

Installation

1. Download the zip file from the above link, and unzip it to a temporary location.
2. If you have an earlier version of PathwayBrowser, uninstall it before installing the new version of PathwayBrowser. To uninstall the earlier version of PathwayBrowser, go to: control panel->add/remove software.
3. To install the PathwayBrowser 2.0, click Setup.exe.

Starting the application

1. After the Pathway Browser 2.0 is successfully installed, a shortcut "PathwayBrowser 2.0" appears on your desktop. To run the application, click on "PathwayBrowser 2.0" on your desktop.
2. To view pathways, right-click on the "Pathway" node on the left panel of user interface, and click a menu item from the short cut menu. Right-clicking on any node on the tree view will display the popup menu.

Uninstallation

Control panel->Add/remove software->PathwayBrowser 2.0->remove

Questions and Comments

       pathcase \at\ case \dot\ edu